Contacts of the helix formed by residues 469 - 495 (chain C) in PDB entry 3RMD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 469 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ASN* 3.0 17.4 + - - -
426C SER* 3.9 6.1 - - - -
428C GLU* 3.6 6.7 - - - -
429C THR* 3.5 22.4 - - - +
468C ASP* 1.3 74.1 - - - +
470C VAL* 1.3 59.7 + - - -
472C PRO* 3.5 10.1 - - - +
473C THR* 2.8 27.9 + - - -
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Residues in contact with VAL 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.8 26.2 - - + +
369C ILE* 4.0 23.3 - - + -
373C LEU* 4.0 27.1 - - + -
378C LYS* 5.8 3.4 - - - +
426C SER* 3.3 6.5 + - - +
428C GLU* 3.6 20.9 - - - +
469C GLY* 1.3 70.3 - - - +
471C VAL* 1.3 64.9 + - + +
473C THR* 2.8 23.5 + - - -
474C GLU* 3.2 19.1 + - - +
577C TYR* 5.0 6.3 - - + -
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Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C ILE* 5.2 9.6 - - + -
420C ILE* 3.9 18.6 - - + -
425C ILE 3.9 5.2 - - - +
426C SER* 3.4 13.2 - - - +
427C PRO* 4.1 13.5 - - + -
470C VAL* 1.3 79.9 - - + +
472C PRO* 1.3 69.9 - - + +
473C THR 3.0 1.0 + - - -
474C GLU* 3.5 4.2 + - - +
475C ILE* 3.1 23.7 + - - +
566C LEU* 4.1 21.9 - - + +
570C LEU* 4.3 26.9 - - + -
577C TYR* 4.7 11.7 - - + -
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Residues in contact with PRO 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C ILE* 3.7 24.2 - - + +
421C ARG* 3.9 10.3 - - + +
424C ASN* 3.8 23.6 - - - +
425C ILE 3.5 20.0 - - - +
426C SER* 3.7 2.5 - - - +
468C ASP* 5.4 3.6 - - + -
469C GLY 3.5 17.9 - - - +
471C VAL* 1.3 94.9 - - + +
473C THR* 1.3 56.1 + - - +
475C ILE* 2.9 14.4 - - + +
476C THR* 2.8 26.2 + - - -
677C LYS* 6.1 1.1 - - - -
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Residues in contact with THR 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C GLN* 6.3 0.9 - - - +
468C ASP* 3.3 22.1 + - - +
469C GLY 2.8 16.1 + - - -
470C VAL* 2.8 11.3 + - - -
472C PRO* 1.3 75.8 - - - +
474C GLU* 1.3 72.0 + - - +
475C ILE 3.1 1.1 - - - -
476C THR* 3.0 6.1 + - - -
477C LYS* 2.8 31.0 + - + +
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Residues in contact with GLU 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TRP* 4.2 13.5 - - + -
368C ILE* 4.5 10.1 - - + +
369C ILE* 4.3 22.5 - - + +
372C SER* 2.7 26.1 + - - +
373C LEU* 5.2 1.0 - - - +
376C GLN* 5.1 3.6 + - - -
470C VAL* 3.2 25.4 + - - +
471C VAL* 4.2 6.3 - - - +
473C THR* 1.3 88.5 - - - +
475C ILE* 1.3 63.5 + - - +
477C LYS* 2.6 40.8 + - - +
478C VAL* 3.1 29.5 + - + +
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Residues in contact with ILE 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TRP* 4.8 6.2 - - + -
417C PRO* 4.0 31.6 - - + +
420C ILE* 4.6 4.3 - - + -
421C ARG* 3.6 17.9 - - + -
471C VAL 3.1 16.1 + - - +
472C PRO* 2.9 26.5 - - + +
474C GLU* 1.3 76.5 - - - +
476C THR* 1.3 68.7 + - - +
478C VAL* 3.0 9.7 + - + +
479C PHE* 3.0 27.6 + - + +
563C ILE* 4.1 28.3 - - + +
566C LEU* 3.5 31.2 - - + +
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Residues in contact with THR 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ARG* 2.8 42.0 + - - +
472C PRO 2.8 21.5 + - - -
473C THR* 3.0 6.1 + - - -
475C ILE* 1.3 82.2 - - - +
477C LYS* 1.3 62.8 + - - +
479C PHE* 3.3 7.7 + - - +
480C ASN* 2.7 44.2 + - - +
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Residues in contact with LYS 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TYR* 5.2 2.9 - - - -
368C ILE* 5.2 6.3 + - - +
372C SER* 3.1 20.6 + - - +
473C THR* 2.8 14.4 + - + +
474C GLU* 2.6 42.3 + - - +
476C THR* 1.3 78.7 - - - +
478C VAL* 1.3 57.6 + - - +
480C ASN* 3.2 9.4 + - - +
481C GLN* 2.9 54.3 + - + +
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Residues in contact with VAL 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TYR* 4.0 17.7 - - + +
365C TRP* 3.8 24.0 - - + -
368C ILE* 5.4 2.9 - - + -
474C GLU 3.2 14.4 - - - +
475C ILE* 3.0 6.9 + - + +
477C LYS* 1.3 78.1 - - + +
479C PHE* 1.3 60.3 + - - +
481C GLN* 3.6 9.5 + - - +
482C ARG* 3.4 20.8 + - - +
559C ARG* 3.6 42.5 - - - +
562C LEU* 4.2 11.4 - - + -
563C ILE* 3.9 10.1 - - + +
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Residues in contact with PHE 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C THR* 5.0 9.0 - - + -
414C SER* 3.3 33.2 - - - -
417C PRO* 4.5 6.7 - - + -
418C SER* 5.0 5.6 - - - -
421C ARG* 3.7 24.5 - - - +
475C ILE* 3.0 18.8 + - + +
476C THR* 3.4 14.6 - - + +
477C LYS 3.1 0.4 - - - -
478C VAL* 1.3 79.2 - - - +
480C ASN* 1.3 61.2 + - - +
482C ARG* 3.8 6.2 - - - +
483C LYS* 3.2 32.7 + - + +
563C ILE* 3.4 41.3 - - + -
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Residues in contact with ASN 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C THR* 2.7 37.3 + - - +
477C LYS* 3.7 8.3 - - - +
479C PHE* 1.3 77.8 - - - +
481C GLN* 1.3 56.4 + - + +
482C ARG 3.1 0.7 - - - -
483C LYS* 3.3 12.0 + - - +
484C GLU* 2.7 39.4 + - - +
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Residues in contact with GLN 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TYR* 2.4 35.7 + - - -
477C LYS* 2.9 49.6 - - + +
478C VAL* 3.7 8.3 - - - +
480C ASN* 1.3 74.7 - - + +
482C ARG* 1.3 55.8 + - - +
484C GLU* 3.1 11.8 - - - +
485C HIS* 2.7 46.0 + - + +
559C ARG* 2.7 39.3 + - - +
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Residues in contact with ARG 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C VAL 3.4 11.0 + - - +
479C PHE* 3.8 12.3 - - - +
481C GLN* 1.3 76.4 - - - +
483C LYS* 1.3 69.1 + - - +
484C GLU 2.6 2.4 + - - -
485C HIS* 2.9 2.6 + - - +
486C LYS* 2.9 46.6 + - - +
556C GLN* 2.8 57.1 + - + +
559C ARG* 3.8 13.2 - - + +
560C LYS* 3.0 40.9 - - - +
563C ILE* 4.3 16.8 - - - -
2J DTP 5.5 3.8 + - - -
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Residues in contact with LYS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C PHE* 3.2 23.3 - - + +
480C ASN* 3.3 16.2 - - - +
482C ARG* 1.3 79.8 - - + +
484C GLU* 1.3 64.5 + - - +
486C LYS* 3.7 20.2 + - - +
487C GLY* 3.5 11.4 + - - -
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Residues in contact with GLU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ASN* 2.7 16.9 + - - +
481C GLN* 3.1 16.4 - - - +
482C ARG 2.6 3.4 + - - -
483C LYS* 1.3 70.2 - - - +
485C HIS* 1.3 70.5 + - - +
486C LYS 2.6 16.0 + - - -
487C GLY* 2.7 17.0 + - - -
488C TYR* 3.0 44.8 + - + -
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Residues in contact with HIS 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 6.2 0.4 + - - -
481C GLN* 2.7 33.8 + - + +
482C ARG 4.1 1.6 - - - +
484C GLU* 1.3 89.0 - - - +
486C LYS* 1.3 56.5 + - - +
488C TYR* 3.3 29.0 - + + +
489C MET* 3.1 24.6 + - - +
551C ALA 5.1 1.8 - - - -
552C GLY* 3.9 18.2 - - - +
555C ALA* 3.2 28.9 - - + +
556C GLN* 4.3 8.5 - - - +
559C ARG* 3.2 26.7 + - - -
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Residues in contact with LYS 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ARG* 2.9 47.4 + - - +
483C LYS* 3.7 20.4 - - - +
484C GLU 2.6 6.3 + - - -
485C HIS* 1.3 71.0 - - - +
487C GLY* 1.3 52.7 + - - +
489C MET* 2.8 20.5 + - + +
490C LEU* 2.5 37.4 + - - +
556C GLN* 3.2 30.3 + - + +
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Residues in contact with GLY 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C LYS 3.5 5.6 + - - -
484C GLU 2.7 10.8 + - - -
486C LYS* 1.3 71.0 - - - +
488C TYR* 1.3 63.9 + - - +
489C MET 2.9 5.8 + - - -
490C LEU* 3.8 17.2 - - - +
491C ALA* 3.2 24.4 + - - +
494C ARG* 4.7 2.2 + - - -
519C ARG 4.4 1.5 - - - +
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Residues in contact with TYR 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C GLU* 3.0 46.4 + - + -
485C HIS* 3.3 35.7 - + + +
487C GLY* 1.3 77.5 - - - +
489C MET* 1.3 56.3 + - - +
491C ALA* 4.3 1.6 - - - -
492C ALA* 3.9 17.8 + - - +
519C ARG* 3.0 72.0 + - + +
520C PHE* 4.4 15.8 - + - -
548C THR 3.9 6.4 - - - +
552C GLY* 5.1 5.3 - - - -
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Residues in contact with MET 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C HIS 3.1 9.7 + - - +
486C LYS* 2.8 32.9 + - + +
488C TYR* 1.3 78.5 - - - +
490C LEU* 1.3 54.3 + - - +
491C ALA 2.7 15.8 + - - -
492C ALA* 3.4 8.6 + - - +
493C GLN* 3.3 45.7 + - + +
548C THR 5.1 0.4 - - - -
549C GLU* 4.1 13.9 - - + +
552C GLY* 4.1 7.4 - - - -
553C MET* 3.4 59.5 - - + +
556C GLN* 4.6 0.4 - - + -
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Residues in contact with LEU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C LYS 2.5 19.2 + - - +
487C GLY* 3.8 14.8 - - - +
489C MET* 1.3 72.9 - - - +
491C ALA* 1.3 50.0 + - - +
493C GLN* 4.5 8.2 - - - +
494C ARG* 2.6 68.5 + - + +
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Residues in contact with ALA 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C GLY 3.2 14.0 + - - +
488C TYR 4.4 0.4 - - - +
489C MET 2.7 1.6 + - - -
490C LEU* 1.3 78.1 - - - +
492C ALA* 1.3 54.9 + - - +
493C GLN 2.4 19.4 + - - -
494C ARG* 3.0 17.2 + - - +
495C ASN* 3.0 26.0 + - - +
518C TYR 3.7 14.6 - - - +
519C ARG 4.1 9.4 - - - +
521C ASP 3.9 19.1 - - - +
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Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C TYR 3.9 7.2 + - - +
489C MET* 3.4 3.9 + - - +
491C ALA* 1.3 74.5 - - - +
493C GLN* 1.3 59.8 + - - +
495C ASN* 5.1 1.3 - - - -
496C GLY* 3.7 13.5 + - - +
518C TYR* 3.6 13.4 + - + -
542C LEU* 5.9 0.2 - - - +
545C ALA* 2.9 31.0 - - - +
548C THR* 3.1 41.5 - - + +
549C GLU* 3.6 11.2 - - - +
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Residues in contact with GLN 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C MET* 3.3 46.9 + - - +
490C LEU* 4.4 5.8 - - - +
491C ALA 2.4 14.3 + - - -
492C ALA* 1.3 66.8 - - - +
494C ARG* 1.3 56.2 + - + +
495C ASN 2.6 15.9 + - - -
496C GLY* 2.7 12.8 + - - -
497C GLU* 3.1 16.4 + - - +
549C GLU* 3.0 35.3 - - + +
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Residues in contact with ARG 494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C GLY* 4.7 2.0 + - - -
490C LEU* 2.6 67.1 + - + +
491C ALA* 3.0 16.9 - - - +
493C GLN* 1.3 76.9 - - + +
495C ASN* 1.3 86.1 + - - +
497C GLU* 4.8 7.2 - - - -
498C ILE* 4.8 12.3 + - - +
521C ASP* 4.6 15.0 + - - +
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Residues in contact with ASN 495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C ALA* 3.0 11.7 + - - +
492C ALA 5.1 0.4 - - - -
493C GLN 2.6 7.3 + - - -
494C ARG* 1.3 105.2 - - - +
496C GLY* 1.3 56.6 + - - +
497C GLU 3.5 0.7 - - - -
498C ILE* 3.0 29.8 - - - +
499C ILE* 4.5 1.7 - - - +
520C PHE 5.0 0.2 - - - +
521C ASP* 2.9 28.2 - - - +
522C PHE* 2.7 63.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il